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GeneBe API Showcase
This page demonstrates how to use the GeneBe API to query variant information. The API provides programmatic access to genomic annotations and variant data.
API presented here should be used for checking single variants. If you want to check many variants at once, please use other API endpoints that you will find in the documentation.
Documentation & Advanced Usage
• Complete API documentation:docs.genebe.net/docs/api/overview/
• Interactive endpoint tester:api.genebe.net/cloud/gb-api-doc/swagger-ui/
• Python client for pandas:pypi.org/project/genebe/
• Java CLI for VCF files:github.com/pstawinski/genebe-cli
• All tools documented at:docs.genebe.net
API Request Examples for Variant: 11-116847512-T-A (hg38)
Bash / cURL Example
bash
curl "https://api.genebe.net/cloud/api-public/v1/variant?chr=11&pos=116847512&ref=T&alt=A&genome=hg38&allGenes=true"API Response
json
{
"variants": [
{
"chr": "11",
"pos": 116847512,
"ref": "T",
"alt": "A",
"effect": "missense_variant",
"transcript": "NM_001366686.3",
"consequences": [
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIK3",
"gene_hgnc_id": 29165,
"hgvs_c": "c.3916A>T",
"hgvs_p": "p.Met1306Leu",
"transcript": "NM_001366686.3",
"protein_id": "NP_001353615.1",
"transcript_support_level": null,
"aa_start": 1306,
"aa_end": null,
"aa_length": 1369,
"cds_start": 3916,
"cds_end": null,
"cds_length": 4110,
"cdna_start": 3929,
"cdna_end": null,
"cdna_length": 6364,
"mane_select": "ENST00000445177.6",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": true,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIK3",
"gene_hgnc_id": 29165,
"hgvs_c": "c.3916A>T",
"hgvs_p": "p.Met1306Leu",
"transcript": "ENST00000445177.6",
"protein_id": "ENSP00000391295.2",
"transcript_support_level": 5,
"aa_start": 1306,
"aa_end": null,
"aa_length": 1369,
"cds_start": 3916,
"cds_end": null,
"cds_length": 4110,
"cdna_start": 3929,
"cdna_end": null,
"cdna_length": 6364,
"mane_select": "NM_001366686.3",
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIK3",
"gene_hgnc_id": 29165,
"hgvs_c": "c.3592A>T",
"hgvs_p": "p.Met1198Leu",
"transcript": "ENST00000446921.6",
"protein_id": "ENSP00000390442.2",
"transcript_support_level": 1,
"aa_start": 1198,
"aa_end": null,
"aa_length": 1261,
"cds_start": 3592,
"cds_end": null,
"cds_length": 3786,
"cdna_start": 3614,
"cdna_end": null,
"cdna_length": 3858,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIK3",
"gene_hgnc_id": 29165,
"hgvs_c": "n.*3116A>T",
"hgvs_p": null,
"transcript": "ENST00000415541.5",
"protein_id": "ENSP00000392761.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3816,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
"exon_rank_end": null,
"exon_count": 10,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIK3",
"gene_hgnc_id": 29165,
"hgvs_c": "n.1785A>T",
"hgvs_p": null,
"transcript": "ENST00000488337.5",
"protein_id": null,
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 4220,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": null,
"aa_alt": null,
"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"3_prime_UTR_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIK3",
"gene_hgnc_id": 29165,
"hgvs_c": "n.*3116A>T",
"hgvs_p": null,
"transcript": "ENST00000415541.5",
"protein_id": "ENSP00000392761.1",
"transcript_support_level": 1,
"aa_start": null,
"aa_end": null,
"aa_length": null,
"cds_start": -4,
"cds_end": null,
"cds_length": null,
"cdna_start": null,
"cdna_end": null,
"cdna_length": 3816,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIK3",
"gene_hgnc_id": 29165,
"hgvs_c": "c.3772A>T",
"hgvs_p": "p.Met1258Leu",
"transcript": "NM_025164.6",
"protein_id": "NP_079440.3",
"transcript_support_level": null,
"aa_start": 1258,
"aa_end": null,
"aa_length": 1321,
"cds_start": 3772,
"cds_end": null,
"cds_length": 3966,
"cdna_start": 3785,
"cdna_end": null,
"cdna_length": 6212,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIK3",
"gene_hgnc_id": 29165,
"hgvs_c": "c.3772A>T",
"hgvs_p": "p.Met1258Leu",
"transcript": "ENST00000375300.6",
"protein_id": "ENSP00000364449.1",
"transcript_support_level": 2,
"aa_start": 1258,
"aa_end": null,
"aa_length": 1321,
"cds_start": 3772,
"cds_end": null,
"cds_length": 3966,
"cdna_start": 3785,
"cdna_end": null,
"cdna_length": 6207,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIK3",
"gene_hgnc_id": 29165,
"hgvs_c": "c.3592A>T",
"hgvs_p": "p.Met1198Leu",
"transcript": "NM_001281749.3",
"protein_id": "NP_001268678.1",
"transcript_support_level": null,
"aa_start": 1198,
"aa_end": null,
"aa_length": 1261,
"cds_start": 3592,
"cds_end": null,
"cds_length": 3786,
"cdna_start": 3605,
"cdna_end": null,
"cdna_length": 6032,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIK3",
"gene_hgnc_id": 29165,
"hgvs_c": "c.3115A>T",
"hgvs_p": "p.Met1039Leu",
"transcript": "NM_001281748.3",
"protein_id": "NP_001268677.1",
"transcript_support_level": null,
"aa_start": 1039,
"aa_end": null,
"aa_length": 1102,
"cds_start": 3115,
"cds_end": null,
"cds_length": 3309,
"cdna_start": 3729,
"cdna_end": null,
"cdna_length": 6156,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 2,
"exon_rank_end": null,
"exon_count": 4,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIK3",
"gene_hgnc_id": 29165,
"hgvs_c": "c.115A>T",
"hgvs_p": "p.Met39Leu",
"transcript": "ENST00000454905.5",
"protein_id": "ENSP00000392849.1",
"transcript_support_level": 5,
"aa_start": 39,
"aa_end": null,
"aa_length": 70,
"cds_start": 115,
"cds_end": null,
"cds_length": 213,
"cdna_start": 116,
"cdna_end": null,
"cdna_length": 294,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIK3",
"gene_hgnc_id": 29165,
"hgvs_c": "c.3916A>T",
"hgvs_p": "p.Met1306Leu",
"transcript": "XM_047426671.1",
"protein_id": "XP_047282627.1",
"transcript_support_level": null,
"aa_start": 1306,
"aa_end": null,
"aa_length": 1369,
"cds_start": 3916,
"cds_end": null,
"cds_length": 4110,
"cdna_start": 3929,
"cdna_end": null,
"cdna_length": 4142,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIK3",
"gene_hgnc_id": 29165,
"hgvs_c": "c.3772A>T",
"hgvs_p": "p.Met1258Leu",
"transcript": "XM_005271482.5",
"protein_id": "XP_005271539.2",
"transcript_support_level": null,
"aa_start": 1258,
"aa_end": null,
"aa_length": 1321,
"cds_start": 3772,
"cds_end": null,
"cds_length": 3966,
"cdna_start": 3785,
"cdna_end": null,
"cdna_length": 6220,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIK3",
"gene_hgnc_id": 29165,
"hgvs_c": "c.3736A>T",
"hgvs_p": "p.Met1246Leu",
"transcript": "XM_011542722.2",
"protein_id": "XP_011541024.1",
"transcript_support_level": null,
"aa_start": 1246,
"aa_end": null,
"aa_length": 1309,
"cds_start": 3736,
"cds_end": null,
"cds_length": 3930,
"cdna_start": 3749,
"cdna_end": null,
"cdna_length": 6184,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIK3",
"gene_hgnc_id": 29165,
"hgvs_c": "c.3628A>T",
"hgvs_p": "p.Met1210Leu",
"transcript": "XM_047426672.1",
"protein_id": "XP_047282628.1",
"transcript_support_level": null,
"aa_start": 1210,
"aa_end": null,
"aa_length": 1273,
"cds_start": 3628,
"cds_end": null,
"cds_length": 3822,
"cdna_start": 3641,
"cdna_end": null,
"cdna_length": 6076,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIK3",
"gene_hgnc_id": 29165,
"hgvs_c": "c.3592A>T",
"hgvs_p": "p.Met1198Leu",
"transcript": "XM_005271484.4",
"protein_id": "XP_005271541.2",
"transcript_support_level": null,
"aa_start": 1198,
"aa_end": null,
"aa_length": 1261,
"cds_start": 3592,
"cds_end": null,
"cds_length": 3786,
"cdna_start": 3605,
"cdna_end": null,
"cdna_length": 6040,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIK3",
"gene_hgnc_id": 29165,
"hgvs_c": "c.3448A>T",
"hgvs_p": "p.Met1150Leu",
"transcript": "XM_017017424.2",
"protein_id": "XP_016872913.1",
"transcript_support_level": null,
"aa_start": 1150,
"aa_end": null,
"aa_length": 1213,
"cds_start": 3448,
"cds_end": null,
"cds_length": 3642,
"cdna_start": 3461,
"cdna_end": null,
"cdna_length": 5896,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIK3",
"gene_hgnc_id": 29165,
"hgvs_c": "c.3439A>T",
"hgvs_p": "p.Met1147Leu",
"transcript": "XM_011542723.3",
"protein_id": "XP_011541025.1",
"transcript_support_level": null,
"aa_start": 1147,
"aa_end": null,
"aa_length": 1210,
"cds_start": 3439,
"cds_end": null,
"cds_length": 3633,
"cdna_start": 3802,
"cdna_end": null,
"cdna_length": 6237,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 22,
"exon_rank_end": null,
"exon_count": 24,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIK3",
"gene_hgnc_id": 29165,
"hgvs_c": "c.3439A>T",
"hgvs_p": "p.Met1147Leu",
"transcript": "XM_011542724.3",
"protein_id": "XP_011541026.1",
"transcript_support_level": null,
"aa_start": 1147,
"aa_end": null,
"aa_length": 1210,
"cds_start": 3439,
"cds_end": null,
"cds_length": 3633,
"cdna_start": 3656,
"cdna_end": null,
"cdna_length": 6091,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIK3",
"gene_hgnc_id": 29165,
"hgvs_c": "c.3439A>T",
"hgvs_p": "p.Met1147Leu",
"transcript": "XM_011542725.3",
"protein_id": "XP_011541027.1",
"transcript_support_level": null,
"aa_start": 1147,
"aa_end": null,
"aa_length": 1210,
"cds_start": 3439,
"cds_end": null,
"cds_length": 3633,
"cdna_start": 3536,
"cdna_end": null,
"cdna_length": 5971,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 23,
"exon_rank_end": null,
"exon_count": 25,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIK3",
"gene_hgnc_id": 29165,
"hgvs_c": "c.3439A>T",
"hgvs_p": "p.Met1147Leu",
"transcript": "XM_017017425.2",
"protein_id": "XP_016872914.1",
"transcript_support_level": null,
"aa_start": 1147,
"aa_end": null,
"aa_length": 1210,
"cds_start": 3439,
"cds_end": null,
"cds_length": 3633,
"cdna_start": 6941,
"cdna_end": null,
"cdna_length": 9376,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 21,
"exon_rank_end": null,
"exon_count": 23,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIK3",
"gene_hgnc_id": 29165,
"hgvs_c": "c.3439A>T",
"hgvs_p": "p.Met1147Leu",
"transcript": "XM_017017426.2",
"protein_id": "XP_016872915.1",
"transcript_support_level": null,
"aa_start": 1147,
"aa_end": null,
"aa_length": 1210,
"cds_start": 3439,
"cds_end": null,
"cds_length": 3633,
"cdna_start": 3871,
"cdna_end": null,
"cdna_length": 6306,
"mane_select": null,
"mane_plus": null,
"biotype": null,
"feature": null
},
{
"aa_ref": "M",
"aa_alt": "L",
"canonical": false,
"protein_coding": true,
"strand": false,
"consequences": [
"missense_variant"
],
"exon_rank": 10,
"exon_rank_end": null,
"exon_count": 12,
"intron_rank": null,
"intron_rank_end": null,
"gene_symbol": "SIK3",
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"cdna_start": 2292,
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"feature": null
},
{
"aa_ref": "M",
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"protein_coding": true,
"strand": false,
"consequences": [
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],
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"exon_count": 11,
"intron_rank": null,
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"gene_symbol": "SIK3",
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},
{
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"canonical": false,
"protein_coding": false,
"strand": false,
"consequences": [
"non_coding_transcript_exon_variant"
],
"exon_rank": 8,
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"exon_count": 10,
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"gene_symbol": "SIK3",
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"transcript": "ENST00000465421.5",
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},
{
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"protein_coding": false,
"strand": true,
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"intron_variant"
],
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"exon_count": 2,
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"gene_symbol": "APOA1-AS",
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"feature": null
},
{
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"strand": true,
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"intron_variant"
],
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"gene_symbol": "APOA1-AS",
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},
{
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"protein_coding": false,
"strand": true,
"consequences": [
"intron_variant"
],
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"gene_symbol": "APOA1-AS",
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"transcript": "NR_126362.1",
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}
],
"gene_symbol": "SIK3",
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"dbsnp": "rs150218961",
"frequency_reference_population": 0.000011151366,
"hom_count_reference_population": 1,
"allele_count_reference_population": 18,
"gnomad_exomes_af": 0.0000116288,
"gnomad_genomes_af": 0.00000656737,
"gnomad_exomes_ac": 17,
"gnomad_genomes_ac": 1,
"gnomad_exomes_homalt": 1,
"gnomad_genomes_homalt": 0,
"gnomad_mito_homoplasmic": null,
"gnomad_mito_heteroplasmic": null,
"computational_score_selected": 0.18592849373817444,
"computational_prediction_selected": "Benign",
"computational_source_selected": "MetaRNN",
"splice_score_selected": 0.019999999552965164,
"splice_prediction_selected": "Benign",
"splice_source_selected": "max_spliceai",
"revel_score": 0.192,
"revel_prediction": "Benign",
"alphamissense_score": 0.1178,
"alphamissense_prediction": null,
"bayesdelnoaf_score": -0.21,
"bayesdelnoaf_prediction": "Benign",
"phylop100way_score": 5.372,
"phylop100way_prediction": "Uncertain_significance",
"spliceai_max_score": 0.02,
"spliceai_max_prediction": "Benign",
"dbscsnv_ada_score": null,
"dbscsnv_ada_prediction": null,
"apogee2_score": null,
"apogee2_prediction": null,
"mitotip_score": null,
"mitotip_prediction": null,
"acmg_score": -2,
"acmg_classification": "Likely_benign",
"acmg_criteria": "BP4_Moderate",
"acmg_by_gene": [
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "NM_001366686.3",
"gene_symbol": "SIK3",
"hgnc_id": 29165,
"effects": [
"missense_variant"
],
"inheritance_mode": "AR,AD,Unknown",
"hgvs_c": "c.3916A>T",
"hgvs_p": "p.Met1306Leu"
},
{
"score": -2,
"benign_score": 2,
"pathogenic_score": 0,
"criteria": [
"BP4_Moderate"
],
"verdict": "Likely_benign",
"transcript": "ENST00000444200.2",
"gene_symbol": "APOA1-AS",
"hgnc_id": 40079,
"effects": [
"intron_variant"
],
"inheritance_mode": "",
"hgvs_c": "n.124-7778T>A",
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}
],
"clinvar_disease": "not specified",
"clinvar_classification": "Uncertain significance",
"clinvar_review_status": "criteria provided, single submitter",
"clinvar_submissions_summary": "US:1",
"phenotype_combined": "not specified",
"pathogenicity_classification_combined": "Uncertain significance",
"custom_annotations": null
}
],
"message": null
}